I really do not think that removing Chaeto from your tank would have any impact on the nitrates and phosphates.
How often are you testing you phosphates and nitrates and what kits are you using and have they expired?
I believe the main thing that can cause a spike is fish, coral, large snail has recently died/ disappeared in your tank.
Your corals use nitrates, phosphates as does coraline algae, and a decline in their growth can lead to an increase in the nutrients in your tank.
I have found that the best way to tell how your hard corals/ coraline algae are doing is to monitor your alkalinity usage. If your alkalinity usage is dropping, basically your measured alkalinity is increasing you could have an issue.
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